From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-biology/clustalw-mpi/Manifest | 1 + .../clustalw-mpi/clustalw-mpi-0.13-r1.ebuild | 36 ++++++++++++++++++++++ sci-biology/clustalw-mpi/files/0.13-gentoo.patch | 23 ++++++++++++++ sci-biology/clustalw-mpi/metadata.xml | 11 +++++++ 4 files changed, 71 insertions(+) create mode 100644 sci-biology/clustalw-mpi/Manifest create mode 100644 sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild create mode 100644 sci-biology/clustalw-mpi/files/0.13-gentoo.patch create mode 100644 sci-biology/clustalw-mpi/metadata.xml (limited to 'sci-biology/clustalw-mpi') diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest new file mode 100644 index 000000000000..b1f7bb630cd0 --- /dev/null +++ b/sci-biology/clustalw-mpi/Manifest @@ -0,0 +1 @@ +DIST clustalw-mpi-0.13.tar.gz 154911 RMD160 9da3e418efcb0cfd0c5df2705ee217b9dacc3917 SHA1 ae5026e8b4ba58bb0caa5643ea90434d9589df5a SHA256 2fcb0dc0001b034f2931153654fc66d67db360f0bf3fbcde19dc389bbe145845 diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild new file mode 100644 index 000000000000..11f1e57e2731 --- /dev/null +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm" +HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php" +SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="public-domain" +IUSE="mpi_njtree static_pairalign" + +DEPEND="virtual/mpi" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + if use mpi_njtree; then + sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ + die "Failed to configure MPI code for NJ trees." + fi + if use static_pairalign; then + sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ + die "Failed to configure static scheduling for pair alignments." + fi +} + +src_install() { + dobin ${PN} + newdoc README.${PN} README +} diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch new file mode 100644 index 000000000000..6e36061cbb39 --- /dev/null +++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch @@ -0,0 +1,23 @@ + Makefile | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index f2107ce..835232b 100644 +--- a/Makefile ++++ b/Makefile +@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE + PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN + #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN + +-CFLAGS = -c -O3 ++CFLAGS += -c + #CFLAGS = -c -O3 -funroll-all-loops +-LFLAGS = -lm ++LIBS = -lm + + clustalw-mpi: $(OBJECTS) +- $(CC) -o $@ $(OBJECTS) $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml new file mode 100644 index 000000000000..905eba1a07b8 --- /dev/null +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -0,0 +1,11 @@ + + + +sci-biology + + Use MPI (as opposed to serial) code for computing + neighbor-joining trees + Use static (as opposed to dynamic) scheduling + for pair alignments + + -- cgit v1.2.3-65-gdbad